MolNFT v1 · #189265 · protein
Local refinement of SARS-cov-2 S-gamma variant (P.1) rbd and angiotensin-converting enzyme 2 (ACE2) ectodomain
7V84 · Spike glycoprotein: “Local refinement of SARS-cov-2 S-gamma variant (P.1) rbd and angiotensin-converting enzyme 2 (ACE2) ectodomain”. Electron microscopy, 1 ligand (NAG), 8 pockets (best druggability 0.65). MolNFT v1 #189265 on…
- PDB
- 7V84
- Type
- protein
- Length
- 797 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Angiotensin-converting enzyme 2,GREEN fluorescent protein
- EC
- 3.4.17.23, 3.4.17.-
- UniProt
- P0DTC2, Q9BYF1
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.65
Structure
electron microscopy · 2 distinct chains · 44% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 201 | 14% helix, 25% strand | P0DTC2 |
| F | Angiotensin-converting enzyme 2,GREEN fluorescent protein (EC 3.4.17.23, 3.4.17.-) | protein | 596 | 54% helix, 3% strand | Q9BYF1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 486 | 0.65 | 0.77 | 44 | empty |
| 2 | 429 | 0.64 | 0.77 | 38 | empty |
| 3 | 324 | 0.60 | 0.77 | 39 | empty |
| 4 | 408 | 0.58 | 0.75 | 70 | empty |
| 5 | 80 | 0.35 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–F · 874 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 7 disulfide (N-glycosylation, disulfide).
Compared structures
- 7V84 · Local refinement of SARS-CoV-2 S-Gamma variant (P.1) RBD and Angiotensin-converting… · the same entry in another collection · chain A against A, TM-score 1.00
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain F against A, TM-score 0.98
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain F against A, TM-score 0.98
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain F against A, TM-score 0.98
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain F against A, TM-score 0.98
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain F against A, TM-score 0.98
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain F against A, TM-score 0.98
- Q9BYF1 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme 2 (Q9BYF1) · a predicted model of the same protein · chain F against A, TM-score 0.95
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0DTC2
- Every structure of UniProt Q9BYF1
- Elsewhere: RCSB PDB 7V84 · PDBe 7V84 · UniProt P0DTC2 · UniProt Q9BYF1
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